Coarse-grained simulations of cholesterol in symmetric lipid bilayers with restraints on cholesterol positions

Membranes consisting of 520 phospholipids varying levels of chain unsaturation together with 56 (10 mol%) cholesterol molecules were simulated at 298 K. The phospholipids had either 2 (DLiPC) or 4 (DAPC) double bonds in both of their chains. The Martini force field [1] was used and the membranes were generated using insane [2]. In the simulations, a flat-bottom potential was applied to the cholesterol molecules to either prevent them from partitioning to the membrane core, or from performing complete flip–flops.

The simulations were run for 10 microsecond using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations).

The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:

Topology files (top) and molecular definitions (itp)

Index files (ndx)

Run parameter files (mdp)

A run input file (tpr)

Trajectory file (xtc) written every 1 ns

Energy file (edr) written every 100 ps

Log file (log)

Final structure file (gro)

Continue point file (cpt)

The files are named LLLL_CG_CHOLXX_RR_TTT.FFF, where

LLLL is the type of phospholipid

CG stands for coarse-grained (All atom data in a separate upload)

CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)

TTT is the temperature

RR is the width of the flat-bottom potential

FFF is the tile type (see above)

Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section. Moreover, md_RR.mdp is common for both lipid types yet activates a different flat-bottom potential based on RR.

[1] DOI: 10.1021/jp071097f

[2] DOI: 10.1021/acs.jctc.5b00209

[3] DOI: 10.1016/j.softx.2015.06.001